The diagnostic utility of RNA-based fusion panel testing ordered by pathologists in challenging cases

Gene fusion identification by RNA-based next-generation sequencing (NGS) provides important information for cancer patients. NGS is commonly initiated by treating oncologists to identify therapeutic options. However, the implications of large fusion panels on tumor classification and diagnosis are underappreciated. We investigated the extent to which these tests aid diagnosis when ordered by pathologists.

We retrospectively reviewed the results of a validated Archer FusionPlex panel ordered by surgical pathologists at our institution, excluding cases tested for therapeutic targets. One hundred thirty-five cases of solid tumors from October 2020 and September 2021 were included. We compared the initial diagnosis to the final diagnosis, which incorporated fusion gene results. We classified the cases into groups based on the degree of contribution of the RNA fusion panel to the final diagnosis.

Among 135 cases, a fusion event was identified in 47 cases, and no fusion event was identified in 88 cases. The results changed the diagnosis in 4 of 135 fusion positive cases (3%). Twenty-one cases (15%) provided a more specific diagnosis, and original diagnosis was confirmed in 17 cases (13%). In the remaining 5 cases (4%), the results identified fusion events of unknown clinical significance.

RNA-based NGS provides significant benefit as an ancillary diagnostic tool. In our cohort, fusion analysis provided a more definitive diagnosis in 25 cases (19%). Our findings demonstrate an important role for pathologists in appropriate utilization of molecular testing, and diagnostic workflows integrating RNA-based NGS will lead to more accurate diagnosis and better patient care.